DynDom - Protein Domain Motions

Phosphoenolpyruvate Carboxykinase [Atp]

(All numbering and residues are taken from first PDB file)

Run Details Domains Sequence Morph Domain Pairs Contact Graph

DynDom run details

Property	Value
Name	Phosphoenolpyruvate Carboxykinase [Atp]
Conformer 1 (PDB)	1yvy (A)
Conformer 2 (PDB)	1ytm (A)
Window Length	5
Minimum ratio	1.0
Minimum domain size	20

Domains

Domain	Size	Backbone RMSD (A)	Residues
1	367	0.91	4 - 239 248 - 349 401 - 429
2	134	1.06	240 - 247 350 - 400 430 - 514

Sequence

`________________________________________________________________________________________________________________________` `1yvy(A) : SLSESLAKYGITGATNIVHNPSHEELFAAETQASLEGFEKGTVTEMGAVNVMTGVYTGRSPKDKFIVKNEASKEIWWTSDEFKNDNKPVTEEAWAQLKALAGKELSNKPLYVVDLFCGAN` `:` `1ytm(A) : SLSESLAKYGITGATNIVHNPSHEELFAAETQASLEGFEKGTVTEMGAVNVMTGVYTGRSPKDKFIVKNEASKEIWWTSDEFKNDNKPVTEEAWAQLKALAGKELSNKPLYVVDLFCGAN` `________________________________________________________________________________________________________________________` `___________________________________________________________________________________________________________________239__` `1yvy(A) : ENTRLKIRFVMEVAWQAHFVTNMFIRPTEEELKGFEPDFVVLNASKAKVENFKELGLNSETAVVFNLAEKMQIILNTWYGGEMKKGMFSMMNFYLPLQGIAAMHCSANTDLEGKNTAIFF` `:` `1ytm(A) : ENTRLKIRFVMEVAWQAHFVTNMFIRPTEEELKGFEPDFVVLNASKAKVENFKELGLNSETAVVFNLAEKMQIILNTWYGGEMKKGMFSMMNFYLPLQGIAAMHCSANTDLEGKNTAIFF` `___________________________________________________________________________________________________________________239__` `___247___________________________________________________________________________________________________349____________` `1yvy(A) : GLSGTGKTTLSTDPKRLLIGDDEHGWDDDGVFNFEGGCYAKVINLSKENEPDIWGAIKRNALLENVTVDANGKVDFADKSVTENTRVSYPIFHIKNIVKPVSKAPAAKRVIFLSADAFGV` `:` `1ytm(A) : GLSGTGKTTLSTDPKRLLIGDDEHGWDDDGVFNFEGGCYAKVINLSKENEPDIWGAIKRNALLENVTVDANGKVDFADKSVTENTRVSYPIFHIKNIVKPVSKAPAAKRVIFLSADAFGV` `___247___________________________________________________________________________________________________349____________` `____________________________________400__________________________429____________________________________________________` `1yvy(A) : LPPVSILSKEQTKYYFLSGFTAK----------pTPTFSSCFGAAFLTLPPTKYAEVLVKRMEASGAKAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIDTANTATIPYFNFTVPTELK` `:` `1ytm(A) : LPPVSILSKEQTKYYFLSGFTAKLAGTERGITEPTPTFSSCFGAAFLTLPPTKYAEVLVKRMEASGAKAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIDTANTATIPYFNFTVPTELK` `____________________________________400__________________________429____________________________________________________` `_____________________________________` `1yvy(A) : GVDTKILDPRNTYADASEWEVKAKDLAERFQKNFKKF` `:` `1ytm(A) : GVDTKILDPRNTYADASEWEVKAKDLAERFQKNFKKF` `_____________________________________`

Morph

This morph was created using the MorphIt_Pro protein morphing technique.
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Domain Pairs

Property	Value
Fixed Domain ( blue )	1
Moving Domain ( red )	2
Rotation Angle (deg)	17.5
Translation (A)	0.5
Closure (%)	95.3
Bending Residues ( green )	239 - 240 247 - 248 349 - 350 400 - 404 429 - 430
Bending Region Analysis

Dynamic Contact Graph

Conformer 1 Contact:
Residue 1 ———› Residue 2

Conformer 2 Contact:
Residue 2 ———› Residue 1

Movement classification: Hinge

PyMOL Script

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